If your startup scans take long to complete, we could try to debug it and narrow it down to the particular file and eventually fix it, if possible. At least you might want to postpone the startup scans until the computer becomes idle instead of having them run immediately after update or startup.

You would first open the ESET Configuration Editor. Then tool down to ESET Smart Security, ESET NOD32 Antivirus>>ESET kernel>>Scheduler Planner>>Scheduler/Planner: Total… Then click Edit on the right hand side. Once you have the Scheduled tasks window open click the default button (Only present in ESET Remote Administrator Version 4.X and higher). Add the first instance of the Automatic startup file check to the list. Once it is on the list click on, mark for deletion (If you wish to remove this task). Then hit ok and save the configuration. Now you can push this configuration as a task to the clients or add it to the default policy.